Finally I've managed to define several assemblies, and build the output with maven.
I've created a small JOGL project using this method here
Here is the assembly for Linux64, for example (located at src/main/assembly folder) :
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>linux-amd64</id>
<formats>
<format>jar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>
<dependencySet>
<useProjectArtifact>false</useProjectArtifact>
<unpack>false</unpack>
<includes>
<include>org.jogamp.jogl:jogl-all:jar:2.2.0</include>
<include>org.jogamp.jogl:jogl-all:jar:natives-linux-amd64:2.2.0</include>
<include>org.jogamp.gluegen:gluegen-rt:jar:2.2.0</include>
<include>org.jogamp.gluegen:gluegen-rt:jar:natives-linux-amd64:2.2.0</include>
</includes>
</dependencySet>
</dependencySets>
</assembly>
And here is my pom.xml :
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.loloof64.java</groupId>
<artifactId>Simple3DCube</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>Simple3DCube</name>
<description>A simple 3D Cube with JOGL</description>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>org.jogamp.gluegen</groupId>
<artifactId>gluegen-rt-main</artifactId>
<version>2.2.0</version>
</dependency>
<dependency>
<groupId>org.jogamp.jogl</groupId>
<artifactId>jogl-all-main</artifactId>
<version>2.2.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4.1</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.loloof64.java.simple_3d_cube.Launcher</mainClass>
<packageName>com.loloof64.java.simple_3d_cube</packageName>
</manifest>
</archive>
<descriptors>
<descriptor>src/main/assembly/windows32-assembly.xml</descriptor>
<descriptor>src/main/assembly/windows64-assembly.xml</descriptor>
<descriptor>src/main/assembly/linux32-assembly.xml</descriptor>
<descriptor>src/main/assembly/linux64-assembly.xml</descriptor>
<descriptor>src/main/assembly/solaris32-assembly.xml</descriptor>
<descriptor>src/main/assembly/solaris64-assembly.xml</descriptor>
<descriptor>src/main/assembly/macosx-universal-assembly.xml</descriptor>
</descriptors>
</configuration>
</plugin>
</plugins>
</build>
</project>